computeKsPipeline: Runs the pipeline to compute the Ks values of gene pair 'x'...

In asishallab/GeneFamilies: Analyses different properties of gene families

Runs the pipeline to compute the Ks values of gene pair 'x' with coding sequences held in 'cds'. Temporary files are stored in 't.d'. Disclaimer: This function will only work on *nix Operating Systems with 'codeml' and 'tail' installed.

Description

Runs the pipeline to compute the Ks values of gene pair 'x' with coding sequences held in 'cds'. Temporary files are stored in 't.d'. Disclaimer: This function will only work on *nix Operating Systems with 'codeml' and 'tail' installed.

Usage

computeKsPipeline(gene.a, gene.b, cds = all.cds,
  t.d = file.path(tempdir(), paste(gene.a, gene.b, sep = "_")),
  codeml.call = getOption("GeneFamilies.codeml.call", "codeml"))

Arguments

gene.a	A string holding the gene identifier as present in argument cds.
gene.b	A string holding the gene identifier as present in argument cds.
cds	an instance of base::list as generated by seqinr::read.fasta holding the unaligned coding sequences of the genes in 'x'. Default is GeneFamilies::all.cds.
t.d	the directory to store the files in, default is tempdir() appended with paste( gene,a, gene.b, collapse='_' )
codeml.call	the call passed to system(...) in order to start codeml. Default is 'codeml', use option 'GeneFamilies.codeml.call' to set another default.

Value

A list of three named numeric values: 'Ka', 'Ks', and 'w'. The first two are parsed from the codeml output file and the latter is computed as Ka/Ks.

References

Yang, Z. and Nielsen, R. (2000) Mol. Biol. Evol., 17, 32-43.

asishallab/GeneFamilies documentation built on May 22, 2023, 11:30 a.m.